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Data for Aboveground rather than belowground productivity drives variability in Miscanthus x giganteus net primary productivity

This dataset contains the data used for the publication “Aboveground rather than belowground productivity drives variability in Miscanthus x giganteus net primary productivity”. This dataset contains Miscanthus x giganteus biomass, carbon, and nitrogen tissue data for aboveground and belowground plant parts collected in 2021 for three different sites in Iowa with three different nitrogen application rates. Data at the Iowa sites were collected via biometric hand harvesting, belowground excavations, and soil coring both in-clump and beside-clump. Data were collected at two collection timepoints to calculate the contributions of belowground parts to Miscanthus x giganteus net primary productivity. This dataset also includes Miscanthus x giganteus and Switchgrass soil coring and excavation data collected in 2012 at the University of Illinois Urbana Champaign Energy Farm.

Belowground Biomass↗

Data from Bioenergy Sorghum Maintains Photosynthetic Capacity in Elevated Ozone Concentrations

Elevated tropospheric ozone concentration (O3) significantly reduces photosynthesis and productivity in several C4 crops including maize, switchgrass and sugarcane. However, it is unknown how O3 affects plant growth, development and productivity in sorghum ( Sorghum bicolor L.), an emerging C4 bioenergy crop. Here, we investigated the effects of elevated O3 on photosynthesis, biomass and nutrient composition of a number of sorghum genotypes over two seasons in the field using free-air concentration enrichment (FACE), and in growth chambers. We also tested if elevated O3 altered the relationship between stomatal conductance and environmental conditions using two common stomatal conductance models. Sorghum genotypes showed significant variability in plant functional traits, including photosynthetic capacity, leaf N content and specific leaf area, but responded similarly to O3. At the FACE experiment, elevated O3 did not alter net CO2 assimilation (A), stomatal conductance (gs), stomatal sensitivity to the environment, chlorophyll fluorescence and plant biomass, but led to reductions in the maximum carboxylation capacity of phosphoenolpyruvate and increased stomatal limitation to A in both years. These findings suggest that bioenergy sorghum is tolerant to O3 and could be used to enhance biomass productivity in O3 polluted regions.

Feedstock Production↗

Data for Complete and Efficient Conversion of Plant Cell Wall Hemicellulose into High-Value Bioproducts by Engineered Yeast

Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae . The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an engineered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.

Conversion↗

Data for Root Exudation Links Root Traits to Soil Functioning in Agroecosystems

Root exudation is a key process for plant nutrient acquisition, but the controls on root exudation and its relationship to soil C and N processes in agroecosystems are unclear. We hypothesized that root exudation rates would be related to root morphological traits, N fertilization, and soil moisture. We also anticipated that root exudation would be correlated with bulk soil enzyme activity. Root exudation, root traits, and bulk soil extracellular enzyme activity were assessed in maize (Zea mays L.), soybean (Glycine max (L.) Merr.), biomass sorghum (Sorghum bicolor (L.) Moench), giant miscanthus (Miscanthus × giganteus), and switchgrass (Panicum virgatum L.). Measurements were taken in situ during two growing seasons with contrasting precipitation regimes, and N fertilization rate was varied in sorghum during one year. Specific root exudation (per unit root surface area) was negatively related to root diameter and was generally higher in annuals than perennials. Sorghum N fertilization did not affect root exudation rates, and soil moisture regime had no effect on annual root exudation rates within maize, sorghum, and miscanthus. Specific root exudation was negatively related to bulk soil C- and N-degrading soil enzyme activities. Intrinsic plant characteristics appeared more important than environmental variables in controlling in situ root exudation rates. The relationships between root diameter, root exudation, and soil C and N processes link root morphological traits to soil functions and demonstrate the potential tradeoffs among plant nutrient acquisition strategies in agroecosystems.

Biomass Analytics↗

Data for Determining Mating Type and Ploidy in Rhodotorula toruloides and its Effect on Growth on Sugars from Lignocellulosic Biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33–9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032–0.131 (g/g) and lipid contents were 13.5–53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

Conversion↗

Similar photosynthetic, but different yield responses of C3 and C4 crops to elevated O3

This dataset contains leaf photosynthetic and biochemical traits, plant biomass, and yield in five C3 crops (chickpea, rice, snap bean, soybean, wheat) and four C4 crops (sorghum, maize, Miscanthus × giganteus, switchgrass) grown under ambient and elevated O3 concentration ([O3]) in the field at free-air O3 concentration enrichment (O3-FACE) facilities over the past 20 years.

C3 and C4 crops↗

Host genotype controls ecological change in the leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass ( Panicum virgatum ). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels

Generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. One of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic hydrolysis. Biomass pretreatment with ionic liquids (ILs) enables efficient saccharification of biomass, but residual ILs inhibit both saccharification and microbial fuel production, requiring extensive washing after IL pretreatment. Pretreatment itself can also produce biomass-derived inhibitory compounds that reduce microbial fuel production. Therefore, there are multiple points in the process from biomass to biofuel production that must be interrogated and optimized to maximize fuel production. Here, we report the development of an IL-tolerant cellulase cocktail by combining thermophilic bacterial glycoside hydrolases produced by a mixed consortia with recombinant glycoside hydrolases. This enzymatic cocktail saccharifies IL-pretreated biomass at higher temperatures and in the presence of much higher IL concentrations than commercial fungal cocktails. Sugars obtained from saccharification of IL-pretreated switchgrass using this cocktail can be converted into biodiesel (fatty acid ethyl-esters or FAEEs) by a metabolically engineered strain of E. coli . During these studies, we found that this biodiesel-producing E. coli strain was sensitive to ILs and inhibitors released by saccharification. This cocktail will enable the development of novel biomass to biofuel bioprocessing configurations that may overcome some of the barriers to production of inexpensive cellulosic biofuels.

09 BIOMASS FUELS↗

Cellulosic Biomass Pretreatment and Sugar Yields as a Function of Biomass Particle Size

Three lignocellulosic pretreatment techniques (ammonia fiber expansion, dilute acid and ionic liquid) are compared with respect to saccharification efficiency, particle size and biomass composition. In particular, the effects of switchgrass particle size (32–200) on each pretreatment regime are examined. Physical properties of untreated and pretreated samples are characterized using crystallinity, surface accessibility measurements and scanning electron microscopy (SEM) imaging. At every particle size tested, ionic liquid (IL) pretreatment results in greater cell wall disruption, reduced crystallinity, increased accessible surface area, and higher saccharification efficiencies compared with dilute acid and AFEX pretreatments. The advantages of using IL pretreatment are greatest at larger particle sizes (.75 mm).

59 BASIC BIOLOGICAL SCIENCES↗

Fast Pyrolysis Behavior of Banagrass as a Function of Temperature and Volatiles Residence Time in a Fluidized Bed Reactor

A reactor was designed and commissioned to study the fast pyrolysis behavior of banagrass as a function of temperature and volatiles residence time. Four temperatures between 400 and 600°C were examined as well as four residence times between ~1.0 and 10 seconds. Pyrolysis product distributions of bio-oil, char and permanent gases were determined at each reaction condition. The elemental composition of the bio-oils and chars was also assessed. The greatest bio-oil yield was recorded when working at 450°C with a volatiles residence time of 1.4 s, ~37 wt% relative to the dry ash free feedstock (excluding pyrolysis water). The amounts of char (organic fraction) and permanent gases under these conditions are ~4 wt% and 8 wt% respectively. The bio-oil yield stated above is for 'dry' bio-oil after rotary evaporation to remove solvent, which results in volatiles and pyrolysis water being removed from the bio-oil. The material removed during drying accounts for the remainder of the pyrolysis products. The 'dry' bio-oil produced under these conditions contains ~56 wt% carbon which is ~40 wt% of the carbon present in the feedstock. The oxygen content of the 450°C, 1.4 s 'dry' bio-oil is ~38 wt%, which accounts for ~33 wt% of the oxygen in the feedstock. At higher temperature or longer residence time less bio-oil and char is recovered and more gas and light volatiles are produced. Increasing the temperature has a more significant effect on product yields and composition than increasing the volatiles residence time. At 600°C and a volatiles residence time of 1.2 seconds the bio-oil yield is ~21 wt% of the daf feedstock, with a carbon content of 64 wt% of the bio-oil. The bio-oil yield from banagrass is significantly lower than from woody biomass or grasses such as switchgrass or miscanthus, but is similar to barley straw. In conclusion, the reason for the low bio-oil yield from banagrass is thought to be related to its high ash content (8.5 wt% dry basis) and high concentration of alkali and alkali earth metals (totaling ~2.8 wt% relative to the dry feedstock) which are catalytic and increase cracking reactions during pyrolysis.

60 APPLIED LIFE SCIENCES↗

Genome assembly of the fungus Cochliobolus miyabeanus , and transcriptome analysis during early stages of infection on American wildrice ( Zizania palustris L.)

Here, the fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice ( Oryza sativa ) and two North American specialty crops, American wildrice ( Zizania palustris ) and switchgrass ( Panicum virgatu ). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N 50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta . A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

Water impacts of U.S. biofuels: Insights from an assessment combining economic and biophysical models

Biofuels policies induce land use changes (LUC), including cropland expansion and crop switching, and this in turn alters water and soil management practices. Policies differ in the extent and type of land use changes they induce and therefore in their impact on water resources. We quantify and compare the spatially varying water impacts of biofuel crops stemming from LUC induced by two different biofuels policies by coupling a biophysical model with an economic model to simulate the economically viable mix of crops, land uses, and crop management choices under alternative policy scenarios. We assess the outputs of an economic model with a high-resolution crop-water model for major agricultural crops and potential cellulosic feedstocks in the US to analyze the impacts of three alternative policy scenarios on water balances: a counterfactual ‘no-biofuels policy’ (BAU) scenario, a volumetric mandate (Mandate) scenario, and a clean fuel-intensity standard (CFS) scenario incentivizing fuels based on their carbon intensities. While both biofuel policies incentivize more biofuels than in the counterfactual, they differ in the mix of corn ethanol and advanced biofuels from miscanthus and switchgrass (more corn ethanol in Mandate and more cellulosic biofuels in CFS). The two policies differ in their impact on irrigated acreage, irrigation demand, groundwater use and runoff. Net irrigation requirements increase 0.7% in Mandate and decrease 3.8% in CFS, but in both scenarios increases are concentrated in regions of Kansas and Nebraska that rely upon the Ogallala aquifer for irrigation water. Our study illustrates the importance of accounting for the overall LUC and shifts in agricultural production and management practices in response to policies when assessing the water impacts of biofuels.

09 BIOMASS FUELS↗

Effects of nitrogen fertilization and bioenergy crop type on topsoil organic carbon and total Nitrogen contents in middle Tennessee USA

Nitrogen (N) fertilization affects bioenergy crop growth and productivity and consequently carbon (C) and N contents in soil, it however remains unclear whether N fertilization and crop type individually or interactively influence soil organic carbon (SOC) and total N (TN). In a three-year long fertilization experiment in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) croplands in Middle Tennessee USA, soil samples (0–15cm) were collected in plots with no N input (NN), low N input (LN: 84 kg N ha -1 yr -1 in urea) and high N input (HN: 168 kg N ha -1 yr -1 in urea). Besides SOC and TN, the aboveground plant biomass was also quantified. In addition to a summary of published root morphology data based on a separated mesocosm experiment, the root leachable dissolved organic matter (DOM) of both crops was also measured using archived samples. Results showed no significant interaction of N fertilization and crop type on SOC, TN or plant aboveground biomass (ABG). Relative to NN, HN (not LN) significantly increased SOC and TN in both crops. Though SG showed a 15–68% significantly higher ABG than GG, GG showed a 9.3–12% significantly higher SOC and TN than SG. The positive linear relationships of SOC or TN with ABG were identified for SG. However, GG showed structurally more complex and less readily decomposed root DOM, a larger root volume, total root length and surface area than SG. Collectively, these suggested that intensive N fertilization could increase C and N stocks in bioenergy cropland soils but these effects may be more likely mediated by the aboveground biomass in SG and root chemistry and morphology in GG. Future studies are expected to examine the root characteristics in different bioenergy croplands under the field fertilization experiment.

54 ENVIRONMENTAL SCIENCES↗

Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae)

We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes.

54 ENVIRONMENTAL SCIENCES↗

Does Plant Biomass Manipulation in Static Chambers Affect Nitrous Oxide Emissions from Soils?

One of the most widespread approaches for measurement of greenhouse gas emissions from soils involves the use of static chambers. This method is relatively inexpensive, is easily replicated, and is ideally suited to plot-based experimental systems. Among its limitations is the loss of detection sensitivity with increasing chamber height, which creates challenges for deployment in systems including tall vegetation. It is not always possible to avoid inclusion of plants within chambers or to extend chamber height to fully accommodate plant growth. Thus, in many systems, such as perennial forages and biomass crops, plants growing within static chambers must either be trimmed or folded during lid closure. Currently, data on how different types of biomass manipulation affect measured results is limited. For this study, we compare the effects of cutting vs. folding of biomass on nitrous oxide measurements in switchgrass (Panicum virgatum L.) and alfalfa (Medicago sativa L.) systems. We report only limited evidence of treatment effects during discrete sampling events and little basis for concern that effects may intensify over time as biomass manipulation is repeatedly imposed. However, nonsignificant treatment effects that were consistently present amounted to significant overall trends in three out of the four systems studied. Such minor disparities in flux could amount to considerable quantities over time, suggesting that caution should be exercised when comparing cumulative emission values from studies using different biomass manipulation strategies.

54 ENVIRONMENTAL SCIENCES↗

Perennialization and Cover Cropping Mitigate Soil Carbon Loss from Residue Harvesting

While the US Midwest is expected to serve as a primary feedstock source for cellulosic biofuel production, the impacts of residue harvesting on soil organic carbon (SOC) may greatly limit sustainable production capacity. However, viable feedstock production could be realized through adoption of management practices and cropping systems that offset residue‐harvest‐induced SOC losses. Sequestration of SOC can be enhanced by increasing the duration of crop soil cover through cover or double cropping or cultivation of dedicated perennials. However, assessing the efficacy of such options across sites and over long periods is experimentally challenging. Hence, we use the Environmental Productivity Integrated Climate (EPIC) model to provide such an assessment. Model‐data integration was used to calibrate and evaluate model suitability, which exhibited reasonable effectiveness through R 2 of 0.97 and 0.63 for SOC stock and yield, respectively. Long‐term simulations indicate considerable capacity for offsetting SOC loss. Incorporating rye ( Secale cereal L.) into continuous corn ( Zea mays L.) and corn–soybean [ Glycine max (L.) Merr.] systems offset the SOC losses induced by harvesting 21.2 and 38.3% of available stover, respectively. Similarly, converting 20.4% of corn–soybean land to miscanthus ( Miscanthus × giganteus J.M. Greef & Deuter ex Hodkinson & Renvoize) or 27.5% of land to switchgrass ( Panicum virgatum L.) offset the SOC impacts of harvesting 60% of stover from the remaining corn–soybean lands. These responses indicate that adoption of such measures would sizably affect the life cycle consequences of residue‐derived biofuels and expand estimates of sustainable cellulosic feedstock production capacity from the US Midwest. Core Ideas EPIC suitably assessed SOC under annual, cover, double, and perennial crops. Perennial cultivation offset the SOC losses of considerable residue harvesting. Rye double crops offset sizable residue‐induced SOC losses. Adoption could greatly expand Midwestern sustainable biofuel production capacity.

Jones, Curtis D.↗

Nitrate Leaching from Continuous Corn, Perennial Grasses, and Poplar in the US Midwest

Leaching from annual corn ( Zea mays L.) crops is a primary source of nitrate (NO 3 - ) pollution of ground and surface waters. Here, we compare NO 3 - losses from no-till corn with losses from various alternative perennial cropping systems (switchgrass [ Panicum virgatum L.], miscanthus [ Miscanthus ×giganteus J.M. Greef & Deuter ex Hodkinson & Renvoiz], a native grass mixture, and restored prairie), as well as hybrid poplar ( Populus nigra L. × P. maximowiczii A. Henry ‘NM6’), all grown on a well-drained soil in Michigan. Soil water was sampled from below the root zone using suction cup samplers during nonfrozen periods (March–November) between 2009 and 2016. Leaching was estimated from NO 3 - concentrations in soil water and modeled drainage (percolation) rates. Drainage rates were not significantly different among crops, constituting ~30% of total annual precipitation. Aboveground net primary production (Mg ha -1 yr -1 ) averaged across the 7 yr was highest in poplar (30.8 ± 1.9 [SE]) followed by miscanthus (23.9 ± 2.4) and corn (20.4 ± 0.9). Volume-weighted mean NO 3 - concentrations (mg N L -1 ) and NO 3 - leaching (kg ha -1 yr -1 ) averaged across the 7 yr were 9.2 and 34.1, 2.3 and 5.9, and 3.0 and 7.2, respectively, for corn, perennial grasses and poplar. Approximately 10 to 32% of applied N was lost as NO 3 - from these crops, with the highest percent losses from poplar (32%) followed by corn (20%). Perennial cropping systems leached considerably more NO 3 - in first few years after planting, but over 7 yr they lost much less NO 3 - than corn. Perennial crops may therefore help ameliorate NO 3 - pollution in agricultural landscapes even if they receive modest N fertilization.

54 ENVIRONMENTAL SCIENCES↗

Legume Addition to Perennial Warm‐Season Grass Swards Increases Harvested Biomass

The adoption of perennial warm‐season grass crops for bioenergy production faces significant social, economic, and agronomic challenges. The inclusion of legumes in warm‐season grass swards may increase productivity, reduce weed pressure and the need for fertilizer inputs, and allow farmers greater management flexibility. The objectives of this study were (i) to evaluate whether the overseeding of red clover ( Trifolium pratense L.) in warm‐season grass swards can improve biomass yields and reduce weed cover, (ii) to determine if biomass yield gains arise from increased N availability or the biomass production of the legume crop, and (iii) to determine whether switchgrass ( Panicum virgatum L.) or big bluestem ( Andropogon gerardii Vitman.) accessions respond differently to red clover overseeding. Once established, red clover addition increased biomass yields in unfertilized swards to levels equivalent to fertilization with 112 kg N ha −1 and reduced weed cover by 7%. The yield gains with clover addition were consistent irrespective of the warm‐season grass accession tested and were attributable to the production of biomass by the clover. The incorporation of legumes in mixtures with perennial warm‐season grasses can and should play a part in improving the viability of these cropping systems. Future studies should consider alternative planting, harvesting, and weed control in a long‐term experimental framework to refine management of legume and warm‐season grass mixtures.

Jakubowski, Andrew R.↗